RegulonDB RegulonDB 11.1: Operon Form
   

ppsA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ppsA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ppsA
Synonym(s): OP00221, pps
Gene(s): ppsA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene ppsA is increased under acidic growth conditions in microaerobiosis Marzan LW,2013 and it is highly increased in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021.
Reference(s): [1] Niersbach M., et al., 1992
Promoter
Name: ppsAp
+1: 1787161
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 49
Sequence: tatatttgcttgaacgattcaccgtttttttcatccggttaaatatgcaaagataaatgcGcagaaatgtgtttctcaaac
                                 -35                  -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Negre D., et al., 1998
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Cra,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra activator ppsAp 1787199 1787215 -45.5 aaaatatattTGCTTGAACGATTCACCgtttttttca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [6], [7], [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Niersbach M., Kreuzaler F., Geerse RH., Postma PW., Hirsch HJ., 1992, Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase., Mol Gen Genet 231(2):332-6

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Negre D., Oudot C., Prost JF., Murakami K., Ishihama A., Cozzone AJ., Cortay JC., 1998, FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli., J Mol Biol 276(2):355-65

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Ramseier TM., Negre D., Cortay JC., Scarabel M., Cozzone AJ., Saier MH., 1993, In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium., J Mol Biol 234(1):28-44

 [6] Sarkar D., Siddiquee KA., Arauzo-Bravo MJ., Oba T., Shimizu K., 2008, Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli., Arch Microbiol 190(5):559-71

 [7] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [8] Son YJ., Phue JN., Trinh LB., Lee SJ., Shiloach J., 2011, The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth., Microb Cell Fact 10:52

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